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r179: changed the preset for assembly alignment

This commit is contained in:
Heng Li 2017-07-17 22:41:46 -04:00
parent 38aa66fa30
commit 941059292e
3 changed files with 20 additions and 6 deletions
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3
README.md
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@ -27,7 +27,8 @@ Minimap2 is the successor of [minimap][minimap]. It uses a similar
minimizer-based indexing and seeding algorithm, and improves the original
minimap with homopolyer-compressed k-mers (see also [SMARTdenovo][smartdenovo]
and [longISLND][longislnd]), better chaining and the ability to produce CIGAR
with fast extension alignment (see also [libgaba][gaba] and [ksw2][ksw2]).
with fast extension alignment (see also [libgaba][gaba] and [ksw2][ksw2]) and
two-piece affine gap cost.
## Limitations

13
main.c
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@ -10,7 +10,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r178-pre"
#define MM_VERSION "2.0-r179-pre"
void liftrlimit()
{
@ -135,8 +135,14 @@ int main(int argc, char *argv[])
is_hpc = 1, k = 19, w = 5;
} else if (strcmp(optarg, "map10k") == 0) {
is_hpc = 1, k = 19;
} else if (strcmp(optarg, "asm1m") == 0) {
} else if (strcmp(optarg, "asm5") == 0) {
k = 19, w = 19;
opt.a = 1, opt.b = 19, opt.q = 39, opt.q2 = 61, opt.e = 2, opt.e2 = 1;
opt.min_dp_max = 200;
} else if (strcmp(optarg, "asm10") == 0) {
k = 19, w = 19;
opt.a = 1, opt.b = 9, opt.q = 16, opt.q2 = 41, opt.e = 2, opt.e2 = 1;
opt.min_dp_max = 200;
} else {
fprintf(stderr, "[E::%s] unknown preset '%s'\n", __func__, optarg);
return 1;
@ -168,7 +174,8 @@ int main(int argc, char *argv[])
fprintf(stderr, " ava-pb: -Hk19 -w5 -Xp0 -m100 -g10000 -K500m --max-chain-skip 25 (PacBio read overlap)\n");
fprintf(stderr, " ava-ont: -k15 -w5 -Xp0 -m100 -g10000 -K500m --max-chain-skip 25 (ONT read overlap)\n");
fprintf(stderr, " map10k: -Hk19 (PacBio/ONT vs reference mapping)\n");
fprintf(stderr, " asm1m: -k19 -w19 (intra-species assembly to ref mapping)\n");
fprintf(stderr, " asm5: -k19 -w19 -A1 -B19 -O39,61 -E2,1 -s200 (assembly to ref mapping; break at 5%% div.)\n");
fprintf(stderr, " asm10: -k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 (assembly to ref mapping; break at 10%% div.)\n");
fprintf(stderr, " Alignment:\n");
fprintf(stderr, " -A INT matching score [%d]\n", opt.a);
fprintf(stderr, " -B INT mismatch penalty [%d]\n", opt.b);

10
minimap2.1
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@ -183,8 +183,14 @@ Oxford Nanopore all-vs-all overlap mapping (-k15 -w5 -Xp0 -m100 -K500m -g10000 -
.B map10k
PacBio/Oxford Nanopore read to reference mapping (-Hk19)
.TP
.B asm1m
Long assembly to reference mapping (-k19 -w19)
.B asm5
Long assembly to reference mapping (-k19 -w19 -A1 -B19 -O39,61 -E2,1 -s200).
Typically, the alignment will not extend to regions with 5% or higher sequence
divergence. Only use this preset if the average divergence is far below 5%.
.TP
.B asm10
Long assembly to reference mapping (-k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200). Up
to 10% sequence divergence.
.RE
.TP
.BI --max-chain-skip \ INT